Serine Proteases – Enzyme Catalysis

With the help of catalysts, chemical reactions are accelerated and the entire human metabolism is thereby brought in momentum. Everything about the various biocatalysts and their classification can be found here.

00:00
Okay. Now, serine proteases, as I said, cleave peptide
bonds, that's the catalytic thing that they do.
00:06
They have specificity of cutting,
again, by binding only to certain proteins.
00:12
They only cut those proteins that they bind.
They have a common active site.
00:18
All the serine proteases, the
different serine proteases have athree dimensional configuration of the place in them
where the reaction occurs.
00:27
Now we will see that
that is important becausethat configuration is what creates the electronic
environment necessary for the reaction to take place.
00:37
And last of all, the serine proteasesare very well studied. So we understand the
mechanism of their action quite well.
00:43
So let's take a look now at the
mechanism of the serine proteases.
00:47
I have shown on the screen here a substratefor the enzyme. This is a
polypeptide chain or proteinthat the serine protease will cut.
00:58
The specific cut is going to occur herewill occur between the carbon and
the nitrogen on this molecule.
01:04
And of course, you know from the structures we
have talked about in the other presentationsthis is the location of the peptide bond.
01:09
Now on the right side of
this image, you can seethe central part of a serine protease.
Now the central part is the place herewhere the reaction is
going to be catalyzed.
01:22
Now it's a little hard to get our
head around at some of these things.
01:25
So you are gonna see in some
cases, I am gonna stretchbonds and stretch molecules a little bitto actually make things fits
so you can understand this.
01:33
Please understand that in an enzyme itself,of course, they are already better positioned,
but it's hard with figuresto make things fit as we would like to.
Serine proteases all have a common featureof their active site. And the common feature
that they have of their active siteis that they all contain these three amino
acids side chains that you can seelocated in close proximity of each other.
01:55
Now I always like to remind students
that when we see something like thisit reminds us that protein folding does occur.
02:04
That is the serine and histidine
and the aspartic acidwhich are the three side
chains that we see hereare not located close to each
other in primary sequence.
02:10
They are brought into close proximity of
each other by the folding of the enzymeto make them physically close
to each other, as we see here.
02:22
And the closeness of these
is important to start.
02:25
But more importantly, the flexibility of the enzyme
with these side chainsis absolutely essential to the catalytic
function that will happen.
02:34
Okay. So we imagine now that
we see this folded enzymeand then the rest of the enzyme is shown
in yellow. We are looking right nowspecifically at the active site.
Near the active site we havea place where the protein is going to bind, and
the protein that's gonna be cut is going to beinteracted with this catalytic triad
of serine, histidine and aspartic acid.
02:56
The binding of the substrate to the enzyme occurs
in a specialized site on the enzyme call the S1 pocket.
03:05
So we have shown here the S1 pocket that is a sort
of a semi circle that's holding on to a part of that protein.
03:12
We can see the protein that is going to
be cut now is at the active site.
03:17
Now in the binding of this
protein to the active siteyou notice that the nitrogen
on the histidine has an arrowpointing towards the hydroxide.
We also note that the oxygen, that is onthe side chain of aspartic acid has a little dot
next to the hydrogen on the histidine.
03:37
What's happened here? Well, then
going from the previous slide to this slide,we can see that what's happened is the
enzyme has changed shape very slightly.
03:48
The binding of the substrate,and remember that binding
of substrate changes enzymes,has changed the enzyme very slightly.
03:56
So that the proximity of aspartic acid's
side chain to histidines has changed.
04:03
That's very important. Aspartic acid here,
the oxygen has a negative charge,and the negative charge has moved a little bit
closer to the ring of the histidine as shown here.
04:15
By this small action, the electronic configuration of
the ring of histidine is changed.
04:23
And it's that change which is causing
now the nitrogen to be reaching outand what it's going to do
is it's going to grabthat hydrogen that's on serine, okay?So this tiny change in shape that
happen on the binding of the enzymeis starting the process by which
the reaction is going to occur.
04:41
So we can see here that the S1 pocket
has facilitated all this happening.
04:46
I should say in the S1 pocket, that the S1
pocket gives the specificity of the enzyme.
04:54
The S1 pocket will not bind to everything.
04:57
It will bind to specific proteins
with specific sequences within them.
05:03
Very very important concept.
If it doesn't encounterthose specific things, it won't bind them and if
won't bind them, of course, there is nothing to react.
05:10
At the end this process will not occur.
Okay. So the slight chart structural changes have happenedand we now see the result of this starting to come into play.
The things, the entities have movedcloser into each other. The electronic environment
has definitely changed by this point.
05:29
And what we see is that that proton that was on
the OH of serine is now associated withthe nitrogen of the histidine ring.
Now this is the first step in this catalyticprocess. Actually the second step if we
count the binding of the substrate.
05:45
This making of the oxygen with a
negative charge on the end of serineis fundamental to this reaction occurring.
05:54
We call this negatively charged oxygen on serine, an alkoxide ion.
Okay? That alkoxide ion that's on serine is extraordinary reactive.
06:04
It's ready to go do business.
06:07
Now we have stretched that S1 pocket
little bit to remind us that againwe are bringing things into closer proximity
and that is important because thealkoxide ion is looking for something
to bind to. It is looking fora nucleus. It's what we call a nucleophile.
06:25
And the nucleus that it is looking for here
is this carbon, which is the arrowthat's being pointed from the oxygen
minus down to the orange carbon.
06:35
So there is actually what's called a chemical attack,
a nucleophilic attack, that's occurring on that carbon.
06:43
We can see that the electronsthat are double bonded to the oxygen are
rearranging, as we see, the arrow being pointed.
06:51
And in the next step of the processwhat will happen is that we are going to
see a rearrangement in the molecule.
06:58
Okay? So we went from this positionto this position. Notice that we had a
carbon with a double bond to an oxygenthat now is a carbon with
a single bond to an oxygen.
07:11
That molecule is chemically unstable.
07:12
It's chemically unstable and a chemically
unstable molecule has to be dealt with,because if it's not dealt with,
it's going to cause problems.
07:21
Well, the enzyme has another
pocket in it to dealwith that unstable molecules
called the oxyanion hole.
07:28
And the oxyanion hole helps that
unstable molecule to fall apartwithout problem. That's pretty cool.
07:36
Okay? It's going to fall apart without
problem and what's gonna happen hereas you can see is the nitrogen in blue
is going to reach up and grab that hydrogenthat was originally grabbed by the histidine side chain,
okay? So this intermediate that's in the oxyanion holeis what we call a Tetrahedral, okay?
And tetrahedrals we know from organic chemistryare what happens when carbon has
those four bonds that you can see here,okay? The peptide bond which is
between the carbon and the nitrogen,is going to be the broken as a
result of nitrogen grabbing that hydrogen.
08:13
Here, nitrogen has grabbed the hydrogen.
The grabbing of the hydrogen from the histidinecause the bond between the carbon
and the nitrogen to break.
08:23
So we have broken the peptide bond .And so part of
the protein, the part of the protein shown in blue,is now free to go and do it's
business. It's released.
08:32
There is nothing attaching it to the
enzymes and it goes and it exits.
08:35
What we have done here is we have actually
gone through the first part of the reaction.
08:42
And in this part of the reaction is what we
call the rapid part of the reaction, okay?The other part of the
protein is attached to serine.
08:51
It's physically attached to serine.
It's a covalent bond at this point.
08:55
Now that covalent bond has to be
broken in order for the other partof the original protein to be released.
09:04
And that's what gonna happen
in the slow step of catalysis.
09:08
Now the slow step of catalysis actually has about the
same number of steps as the fast step of catalysis.
09:14
But other things have to happen including the movement of water
into the active site, in order for this peptide to be released.
09:23
Well, we see that happening here. Water
now has physically moved into theactive site. There is a molecule of water.
And that process that we sawof the nitrogen on histidine taking a proton
is going to repeat itself.
09:36
We see it happening here. We see the arrow from the nitrogen
on the histidine pointing to the hydrogen on water.
09:43
So it's gonna take that hydrogen instead of taking the hydrogen
that is originally took, which is no longer there, on serine.
09:49
What's gonna happen in that process is now
we are gonna have an activated oxygenlike we had with the alkoxide ion except
for here it's gonna be a hydroxide.
10:00
We are gonna have an activated oxygen that
is gonna make a nucleophilic attackon carbon just like we saw before.
10:07
So there is a nucleophilic attack that's going to
happen in the process of this moving forward.
10:13
Here is the attack of the hydroxideand look what happens. We see that the electrons
on oxygen are going to rearrange.
10:22
We create a tetrahedral immediate as we created before.
And now there is the oxyanion hole stabilize in that intermediate.
10:33
We now see that what happens is that oxygenis going to attack the hydrogen on that group and it's
gonna pour away just like the first peptide did.
10:42
When it does that, what happens is the molecule released.
So we see the second half of the polypeptide chain releasedand in addition the enzyme returned back to it's original state.
Gone and as it were.
11:03
The cycle is now complete. So it is about 10
steps going through what I described hereand the important thing to understand about
this is that the enzyme started at one state.
11:13
It went through a transitionand then went back to the original state it was in.
Very much like the process I have already describedbut now you have seen
it in mechanistic terms.
11:22
When we saw the image of the reaction occurring, we
saw these various states that you see on the screen.

About the Lecture

The lecture Serine Proteases – Enzyme Catalysis by Kevin Ahern, PhD is from the course Enzymes and Enzyme Kinetics.

Included Quiz Questions

Why is an enzyme catalysis so effective?

It lowers the energy of activation of a reaction

It changes the Gibbs free energy change of a reaction

It changes the standard Gibbs free energy change of a reaction

It only allows reactions to go forward

Which of the following is true of serine proteases?

They use serine for catalysis in their active sites

They cut target proteins at serine residues

They bind serine during catalysis

They are misnamed because they do not involve serine at all

The catalytic triad of the serine protease is composed of which of the following?

Serine, histidine, and aspartic acid

Serine, glutamic acid, and histidine

Serine, glycine, and aspartic acid

Serine, lysine/ and histidine

Serine, alanine, and selenocysteine

Which of the following site allows for the binding of an unstable intermediate during the proteolytic reaction of serine proteases?

Oxyanion hole

Active site

Allosteric site

S1 pocket

Hydroxide/alkoxide pocket

The specificity of the serine protease is determined by the what?

S1 pocket

oxyanion hole

active site

allosteric site

alkoxide/hydroxide pocket

Which of the following acts as a nucleophile during the catalytic action of a serine protease enzyme?

Alkoxide ion produced on serine

H+ ion

N+ of histidine ring

H+ of serine

O- of aspartic acid

Author of lecture Serine Proteases – Enzyme Catalysis

Kevin Ahern, PhD

Customer reviews

(3)
5,0 of 5 stars

5 Stars

3

4 Stars

0

3 Stars

0

2 Stars

0

1 Star

0

Well explained

By Mary T. on 26. January 2019 for Serine Proteases – Enzyme Catalysis

Attaractively and well explained video of serine protease catalytic mechanism that I have ever seen...Thank you..????

USMLE™ is a joint program of the Federation of State Medical Boards
(FSMB®) and National Board of Medical Examiners (NBME®). MCAT is a registered
trademark of the Association of American Medical Colleges (AAMC).
None of the trademark holders are endorsed by nor affiliated with Lecturio.